Agron. Sustain. Dev. 30 (2010) 359–365c© INRA, EDP Sciences, 2009DOI: 10.1051/agro/2009033

Review article

Available online at:www.agronomy-journal.org

for Sustainable Development

Biogeography of soil microbial communities: a reviewand a description of the ongoing french national initiative

Lionel Ranjard1,2*, Samuel Dequiedt1,2, Claudy Jolivet3, Nicolas P.A. Saby3,Jean Thioulouse4, Jérome Harmand6,7, Patrice Loisel6, Alain Rapaport6, Saliou Fall5, Pascal Simonet5,

Richard Joffre8, Nicolas Chemidlin-Prevost Boure1,2, Pierre-Alain Maron1,2, Christophe Mougel1,2,Manuel P. Martin3, Benoît Toutain3, Dominique Arrouays3, Philippe Lemanceau1,2

1 INRA-Université de Bourgogne, UMR Microbiologie du Sol et de l’Environnement, CMSE, 17 rue Sully, B.V. 86510, 21065 Dijon Cedex, France2 Platform GenoSol, INRA-Université de Bourgogne, CMSE, 17 rue Sully, B.V. 86510, 21065 Dijon Cedex, France

3 INRA Orléans - US 1106, Unité INFOSOL, avenue de la Pomme de Pin, BP 20619, Ardon, 45166 Olivet Cedex, France4 Université de Lyon, 69000 Lyon, France; Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, 69622 Villeurbanne, France

5 Équipe “Génomique Microbienne Environnementale” (Environmental Microbial Genomics Group), UMR CNRS 5005, Laboratoire Ampère,École Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Ecully Cedex, France

6 INRA-INRIA MERE research project, UMR ASB, place Pierre Viala, 34060 Montpellier Cedex, France7 LBE-INRA, UR050, avenue des étangs, 11100 Narbonne, France

8 UMR 5175 CNRS, Équipe DREAM - Centre d’Écologie Fonctionnelle et Évolutive, 1919 route de Mende, 34293 Montpellier Cedex 5, France

(Accepted 19 August 2009)

Abstract – Microbial biogeography is the study of the distribution of microbial diversity on large scales of space and time. This scienceaims at understanding biodiversity regulation and its link with ecosystem biological functioning, goods and services such as maintenance ofproductivity, of soil and atmospheric quality, and of soil health. Although the initial concept dates from the early 20th century (Beijerinck(1913) De infusies en de ontdekking der backterien, in: Jaarboek van de Knoniklijke Akademie van Wetenschappen, Muller, Amsterdam), onlyrecently have an increasing number of studies have investigated the biogeographical patterns of soil microbial diversity. A such delay is due tothe constraints of the microbial models, the need to develop relevant molecular and bioinformatic tools to assess microbial diversity, and thenon-availability of an adequate sampling strategy. Consequently, the conclusions from microbial ecology studies have rarely been generallyapplicable and even the fundamental power-laws differ because the taxa-area relationship and the influence of global and distal parameters onthe spatial distribution of microbial communities have not been examined. In this article we define and discuss the scientific, technical andoperational limits and outcomes resulting from soil microbial biogeography together with the technical and logistical feasibility. The mainresults are that microbial communities are not stochastically distributed on a wide scale and that biogeographical patterns are more influencedby local parameters such as soil type and land use than by distal ones, e.g. climate and geomorphology, contrary to plants and animals. Wethen present the European soil biological survey network, focusing on the French national initiative and the “ECOMIC-RMQS” project. Theobjective of the ECOMIC-RMQS project is to characterise the density and diversity of bacterial communities in all soils in the RMQS libraryin order to assess, for the first time, not only microbial biogeography across the whole of France but also the impact of land use on soilbiodiversity (Réseau de Mesures de la Qualité des Sols = French Soil Quality Monitoring Network, 2200 soils covering all the French territorywith a systematic grid of sampling). The scientific, technical and logistical outputs are examined with a view to the future prospects needed todevelop this scientific domain and its applications in sustainable land use.

soil biogeography / microbial communities / soil survey /microbial ecology / diversity

1. INTRODUCTION

Although microorganisms are the most diverse and abun-dant type of organism on earth (Gans et al., 2005; Curtis

* Corresponding author: ranjard@dijon.inra.fr

and Sloan, 2005), the determinism of microbial diversifica-tion and the distribution of microbial diversity from smallto large scales has been poorly documented and is little un-derstood. Most studies of prokaryote diversification have fo-cused on variations due to mutations and/or lateral gene trans-fers and subsequent selection resulting from environmental

Article published by EDP Sciences

360 L. Ranjard et al.

stresses and competition for resources. Few have consideredmore neutral mechanisms, such as genetic drift due to physi-cal isolation, thus revealing the crucial lack of integration ofthe spatial scale into microbial community assembly (Ranjardand Richaume, 2001; Papke and Ward, 2004).

Ecologists have long recognised that beta-diversity (howcommunity composition changes across a landscape) is pivotalto understanding how environmental factors affect the magni-tude and variability of biodiversity. This conceptual vision isalso relevant to microorganisms since beta-diversity patternsoffer valuable insights into the relative influence of dispersallimitations, environmental heterogeneity, and environmentaland evolutionary changes in shaping the structure of ecolog-ical communities (Green et al., 2004). Although the spatialpatterning of microbial diversity is known to have impor-tant consequences on plant community structure and ecosys-tem functioning, microbial beta-diversity patterns have beenpoorly investigated and remain largely unknown. The empir-ical relationship between the number of species and the areasampled (taxa-area relationship) has not been empirically ex-amined in microorganisms, as it has in plants and animals(Horner-Devine et al., 2004; Green and Bohannan, 2006). Thismay partly be explained by the characteristics of microorgan-isms, namely (i) their small size, which makes access withinenvironmental matrices difficult, (ii) their high density (e.g.more than one billion per gram of soil) and (iii) their hugediversity (from 1000 to 1 000 000 species per gram of soil,Torsvik and Øvreås, 2002), not to mention the complexity ofprecisely defining their species. Progress is also hampered bydifficulties in designing an adequate sampling strategy. Such astrategy needs to integrate a large scale of sampling (region,territory, etc.), with precise squaring that is representative ofany landscape modifications, which therefore implies a verylarge number (several thousands) of samples.

Our aim in this paper is to present the results of the firstanalytical studies of the biogeography of soil microbial com-munities, the concept applied and the technical feasibility ofthis novel scientific domain in environmental microbiology.We shall then describe the European strategy and the Frenchnational soil survey in which different research teams with sci-entific expertise in soil science, statistics, microbial ecologyand geochemistry are, for the first time, working to assess theinventory and mapping of soil microbial diversity on a nationalterritorial scale.

2. SCIENTIFIC OUTCOMES OF MICROBIALBIOGEOGRAPHY

Biogeography is the study of the distribution of biodiver-sity over space and time (Martiny et al., 2006). In other words,the aim in biogeography is to reveal where organisms live andtheir abundance, and to determine those environmental factorsthat select or maintain the presence of these organisms. Thisscientific approach was first applied during the eighteenth cen-tury in studies of the geographic distribution of plant and an-imal diversity. These investigations provided insights into themechanisms that generate and maintain diversity in macroor-

ganisms e.g., speciation, extinction, dispersal and species in-teractions (Brown and Lomolino, 1998).

Despite the key role of microorganisms in a wide rangeof biogeochemical cycles, few studies (in comparison withmacroorganisms) have examined the distribution of microbialdiversity on a broader scale than field plots. The first studydescribing and investigating microbial biogeography was con-ducted by Beijerinck (1913), who stated that “everything iseverywhere, but, the environment selects” (see Sect. 3). Sincethen, few authors have examined the full extent of microbialdiversity or described the biogeographical patterns in an at-tempt to assess this statement and specify which environmen-tal factors exert the strongest influence on indigenous micro-bial communities. Even though recent advances in molecularbiology have led to the development of tools to assess bacte-rial diversity in environmental samples without culturing, moststudies have focused on cataloguing the bacterial diversity inparticular sites or describing how bacterial communities havebeen affected by environmental perturbations (for review seeRanjard et al., 2000). Thus, the conclusions of such microbialecology investigations cannot be generally applied as the datafrom different studies are difficult to compare and the trendsdeduced are often inconsistent.

2.1. Phylogeography of particular populations

To date, most studies dealing with microbial biogeographyhave been limited to the phylo-geography of particular popula-tions, particularly of pathogenic or symbiotic organisms. Oneof the main results is that many host-associated microorgan-isms exhibit genetic and functional patterns that are related tothe distribution of their hosts (for review see Martiny et al.,2006). As regards the free-living microorganisms, most recentinvestigations have been focused on individual soil bacterialstrains (Cho and Tiedje, 2000). These studies have tended todemonstrate that the genetic distance between microorganismsis related to geographic distance, and have highlighted correla-tions between assembly composition and environmental or ge-ographic characteristics (for review see Martiny et al., 2006).Few publications have considered the soil microbial commu-nity as a whole and how it is structured on a large spatial scale.

2.2. Biogeography of microbial communities

In one of the rare studies available, Green et al. (2004)genotyped fungal community structure in numerous Aus-tralian soils (about 1500) and were able to demonstrate thatdespite the high local diversity of microorganisms, the re-gional diversity was only moderate. Fierer and Jackson (2006)produced a continent-scale description of soil bacterial diver-sity by considering about 100 different soils sampled from thenorth to south of America. By applying a DNA fingerprint-ing method, they demonstrated that bacterial diversity was un-related to site temperature, latitude and other variables that,in contrast, strongly influence plant and animal diversity, and

Biogeography of soil microbial communities: a review and a description of the ongoing french national initiative 361

that community composition was largely independent of ge-ographic distance. The environmental factor most influencingbacterial diversity was soil pH, with the highest diversity oc-curring in neutral soils and the lowest in acidic soils. Thesestudies also demonstrated that taxa-area relationships in soilmicroorganisms were weak, thus indicating that microbial bio-geography differs fundamentally from that of “macroorgan-isms”. By applying a pyrosequencing technique to ribosomalsequences in the same set of soil samples, Jones et al. (2009)defined the ecological attributes of particular populations suchas Acidobacteria and confirmed the importance of soil pH intheir dissemination.

In contrast, Johnson et al. (2003) demonstrated that vari-ations in the genetic structure of bacterial communities fromnumerous agricultural soils were not correlated with pH butwith soil texture and electrical conductivity. The overall incon-sistency of these reports may possibly be ascribed to the inade-quate sampling strategy in terms of number and representative-ness of the soils sampled. However, it underlines the fact thatthe number of studies dealing with microbial-biogeographyneeds to be increased to understand the determinism of mi-crobial diversity better, especially as this latter directly affectsa wide range of ecosystem processes and therefore the qualityof our environment.

2.3. The first concept of microbial biogeography:“Beijerinck, 1913”

Microbial ecologists describing biodiversity on a large spa-tial scale, i.e. microbial biogeography, generally invoke one ofthe oldest fundamental paradigms in microbial ecology, “ev-erything is everywhere, but, the environment selects”, pro-posed by Beijerinck (1913). This tenet was used as the start-ing point for studies of prokaryotic biodiversity and theirbiogeographical patterns but was frequently misinterpreted.Baas Becking (1934), and more recently de Witt and Bouvier(2006), rehabilitated the original meaning of this statement,which reflects an apparent contradiction between empiricalobservations that specific microorganisms are observed intheir characteristic environments and the idea that all microor-ganisms are cosmopolitan. Despite the technical difficulty ofverifying the first statement, due to the detection limits ofthe approaches used to characterise microbial diversity, thispremise implies that the genetic cohesiveness of prokaryoticpopulations can never be broken by physical isolation butsolely by adaptation. These basic concepts were only implicitin the publication of Beijerinck (1913) but were tacitly ac-cepted (Baas Becking, 1934).

The concept “everything is everywhere” is supported byseveral particularities of the microbial model: microorganisms(i) are small and easily transported, (ii) are able to form a resis-tant physiological stage that allows them to survive in hostileenvironments, and (iii) have extremely large population sizeswith a high probability of dispersal and a low probability oflocal extinction (Fenchel, 2003). The fact that more than 1018–1020 microorganisms are estimated to be transported annuallythrough the atmosphere between continents supports the hy-

pothesis of a wide dispersion of microbes (Gans et al., 2005).Further evidence is that bacteria can be isolated from placeswhere “they should not be”, e.g. thermophilic bacteria fromcold sea water (Isaksen et al., 1994).

In contrast, “the environment selects” might seem to chal-lenge the concept that “everything is everywhere”, and sug-gests that geographic isolation of populations coupled withlimited dispersal leads to allopatric speciation. An increasingnumber of studies have demonstrated that the physical isola-tion of free-living microorganisms may be more widespreadthan previously thought (for review see Papke and Ward,2004). However, most recent studies have been limited to char-acterisation of the culturable populations which are known torepresent only a very small fraction of the whole community(Amann et al., 1995). To date, few studies have focused on mi-crobial communities, possibly because of the technical limita-tions associated with identifying the huge microbial diversityin natural ecosystems and the difficulties in detecting minorpopulations. These technological limitations have now beenpartly resolved thanks to the recent development of molecu-lar tools that circumvent the isolation and culture of organ-isms, and allow microbial community structure and diversityto be characterised without a priori knowledge (for review seeRanjard et al., 2000; Christen, 2008). Furthermore, these toolsare now generally automated and allow the moderate through-put essential to studies involving the characterisation of nu-merous environmental samples.

3. SOIL BIODIVERSITY MONITORINGIN EUROPE

3.1. International context

Although soil inventory programmes exist in all Europeancountries, there are not many fully operational soil monitoringsystems in Europe (Morvan, 2008). Few include more thanone sampling point in time so that most are mere inventories.The only EU-wide soil monitoring network is the ICP forestlevel 1 grid, which was partly re-sampled in 2006–2007 withinthe Forest Focus BioSoil project (Lacarce et al., 2009). Thedata requirements for this re-sampling did not include micro-bial diversity. Progress in recent years has been hampered by alack of perception of the importance of soil, data ownership is-sues and data incompatibility resulting from the multiplicity ofdifferent sampling and analytical procedures. The ENVASSOproject addressed the need to characterise soils by setting up aseries of interlinked objectives to harmonise the soil data setsthat currently exist in EU Member States (Kibblewhite et al.,2008). Eight threats to soil (erosion, declining organic matter,contamination, compaction, salinisation, loss of biodiversity,soil sealing, landslides and flooding) have been identified inthe European Commission’s official Soil Communication partof the Thematic Strategy for Soil Protection in Europe. Theaim of the ENVASSO project was to develop a system to har-monise existing, mostly national, data sets and provide a cen-tral reference point to assess current soil status and ensure sus-tainable management in the future. This project identified the

362 L. Ranjard et al.

physical and chemical parameters to monitor, most of whichwere already being monitored by the national soil surveys con-ducted in different European countries.

3.2. The French soil survey: RMQS

It was apparent from the initial data collected during theENVASSO project that biodiversity was not fully included inany national soil monitoring network except in the Nether-lands. In 2001, a new structure was created in France to re-organise soil mapping and soil monitoring programmes and toprovide relevant insights into the spatial distribution of soilsand the evolution of their properties. This structure, called theScientific Group on Soils (GIS Sol) includes the Ministriesof Agriculture and Environment, the Environment and En-ergy Management Agency (ADEME), the Research Institutefor Development (IRD), the National Forest Inventory (IFN)and the National Institute of Agronomic Research (INRA).The main soil monitoring programme is the French Soil Qual-ity Network (“Réseau de Mesures de la Qualité des Sols”,RMQS), that is based on a 16 km by 16 km grid, with2200 sites representative of the main soil systems and landuses in France. This configuration has the advantage of be-ing fully compatible with the sites of the ICP forest level 1network (now called BioSoil) which monitors forested soilsacross Europe. The RMQS is a complete and balanced net-work of 2200 sites which will be sampled every 10 years tomonitor soil quality. The primary objectives of the network areto characterise and quantify diffuse contamination in trace el-ements (Saby et al., 2006) and to evaluate and monitor organiccarbon stocks. For this purpose, a set of analyses (particle-size distribution, bulk density, C, N, pH, trace elements, etc.)and a complete description of the soil profile at each site areobtained together with information about past activities, theenvironment, etc. Apart from these objectives, the network isresponsible for many other soil quality evaluations and mon-itoring, e.g. persistent organic pollutants (pesticides, dioxins,organochlorides, PAH, etc.).

3.3. An Ongoing project: The ECOMIC-RMQS project

Based on this soil survey, the scientific project “ECOMIC-RMQS” was set up in 2006, offering the first opportunity toimplement biological diversity in a soil monitoring network.This project is coordinated by the Microbiology of the Soiland Environment Centre (“Centre de Microbiologie du Solet de l’Environnement” i.e. CMSE, INRA Dijon, Burgundy,France) and is one of the first steps to demonstrate the techni-cal feasibility and scientific relevance of federating Europeaninitiatives to monitor soil biodiversity monitoring.

The objective of the ECOMIC-RMQS project is to charac-terise the density, genetic structure and diversity of bacterialcommunities in all soils in the RMQS library (2200 soils sam-pled up to 2009) in order to assess, for the first time, not onlymicrobial biogeography across the whole of France but alsothe impact of land use on soil biodiversity. The strategy for

characterising the density and diversity of the bacterial com-munities relies on molecular tools such as quantitative PCR,DNA micro-array and DNA fingerprinting on soil DNA ex-tracts (Fig. 1).

This integrated project will provide cognitive insights intothe ecological theory on the community assembly by:

– elucidating the relative contribution of geographic isola-tion versus wide dispersal in limiting bacterial diversifica-tion,

– allowing better examination of the taxa-area relationshipfor bacteria,

– deciphering the hierarchy of the environmental parameters(plant cover, physico-chemical characteristics, climate fac-tors, etc.) that most contribute to bacterial community di-versity and composition.

This project should also have more applied outcomes as a re-sult of:

– determining the state of bacterial diversity in French soils,– better estimation of the impact of land use and human ac-

tivities on microbial diversity and distribution,– identifying bacterial bio-indicators specific to land man-

agement and human activities.

The ECOMIC-RMQS project provides an appropriate meansof (i) assessing the microbial-biogeography by use of theRMQS and (ii) elucidating the determinisms of bacterial com-munity diversification in soils better. This project should pro-vide answers to some of the questions originating from mech-anistic hypotheses:

– Are microbial communities a “black box” with no spatialstructure or, like macroorganisms, do they exhibit a par-ticular distribution with predictable, aggregated patternsfrom local to regional scales? In other words, does a taxa-area relationship exist in microbial-biogeography? (Greenet al., 2004; Horner Devine et al., 2004).

– Are spatial variations due to contemporary environmentalfactors or to historical land use and contingencies?

– Which environmental factors (edaphic, climatic, land use,anthropogenic) most contribute to the structure and diver-sity of bacterial communities in soil on very broad geo-graphic scales?The first results obtained in this programme have demon-strated:

– a non-stochastic distribution of bacterial diversity whichis spatially structured in biogeographical patterns on a re-gional scale (Dequiedt et al., 2009),

– a taxa-area relationship for soil bacterial communities,– a positive correlation between bacterial diversification and

landscape diversity and fragmentation,– a greater influence of local environmental local parameters

(pedoclimatic and land use) as opposed to global parame-ters (climate and geomorphology) on bacterial communitydensity and diversity,

– the strongly deleterious effects that specific land use (espe-cially agriculture) can have on indigenous bacterial com-munities.

Biogeography of soil microbial communities: a review and a description of the ongoing french national initiative 363

Figure 1. Schematic description of strategy and outputs of the ECOMIC-RMQS project.

364 L. Ranjard et al.

3.4. Need for technical and logistic supports

One of the main prerequisites of a project such asECOMIC-RMQS, which is aimed to assess microbial diver-sity on a wide scale, is the development of suitable logistics forstoring and managing very large numbers of biological sam-ples and associated data. In addition, the soil samples needto be characterised under medium-throughput conditions withhigh levels of reproducibility and quality of the applied pro-cedures. The GenoSol Platform, which was set up to store andmanage soil samples as well as to ensure molecular characteri-sation of the microbial communities, meets these requirements(Ranjard et al., 2009). Thus, two complementary structuresdescribed as Soil Biological Resource Centres have been de-veloped in France: the INFOSOL Conservatory and GenoSolPlatform.

The INFOSOL unit in Orléans (France) houses the soil con-servatory. This soil library has been designed for the manage-ment, storage, preparation and dissemination of soil samplesfrom the RMQS programme in the long term. Thousands oflarge samples (5 to 10 kg each) are stored air-dried, under con-trolled conditions of temperature and hygrometry. The aim isto provide (i) a memory of the state of French soil, (ii) refer-ence samples for re-analysis after other campaigns, and (iii) asoil bank for research development.

The GenoSol Platform (http://www.dijon.inra.fr/plateforme_genosol) was created in 2008 by the “Centrede Microbiologie du Sol et de l’Environnement” (CMSE,INRA Dijon, Burgundy, France). The aim is to provide anappropriate logistic structure for the acquisition, storageand characterisation of soil genetic resources obtained byextensive sampling (several hundred to several thousandsoils), on very large space and/or time scales (national soilsurvey, long-term experimental sites), and to make theseresources readily available to the scientific community andto policy-makers. The ultimate goal is to produce a reliablereference system based on molecular characterisation (taxo-nomic and functional features) of soil microbial communities,that facilitates the scientific interpretation of sample analyseson large scales of time and space sampling. Another aimof the platform is the long-term storage of a library of soilgenetic resources (soil DNA) to be made available to nationaland international scientific communities (Ranjard et al.,2009). In summary, the GenoSol Platform can be consideredas a logistic and technical tool and therefore as a strategicpartner for research units who wish to benefit from large-scalesoil sampling without needing to develop cumbersome orcircumstantial methodologies or organisations.

In the context of the ECOMIC-RMQS project, the GenoSolPlatform has:

– built up and maintains a national soil DNA library whichis to be made available to the scientific community as awhole in order to assess microbial diversity in the futurewith more powerful tools and/or other molecular analysis,

– developed in collaboration with the INFOSOL conserva-tory a database of the genetic structure and taxonomic di-versity of microbial communities in French soils, so that

an Atlas of Soil Biodiversity can be compiled on a nationalscale,

– established a reference frame for interpreting these anal-yses by (i) treating the determinants of variability of themicrobial communities in soils on a hierarchical basis, and(ii) quantifying the impact of human activities on thesecommunities.

4. CONCLUSION

Various lines in the studies of microbial biogeography cur-rently available could be further developed:

– the scale of investigation could be increased by consider-ing a whole territory or continent to permit better compar-ison of the different pedoclimatic regions,

– widescale soil sampling could be conducted in the longterm to evaluate the influence of land use management andglobal changes on the evolution of soil biodiversity,

– the characterisation of soil microbial diversity could be im-proved by applying recent and innovative techniques suchas pyrosequencing of ribosomal genes to permit exhaus-tive evaluation of the taxonomic diversity of indigenouscommunities (Christen, 2008; Roesch et al., 2007),

– soil biodiversity could be linked with soil functioning toimprove management and protection of the various re-sources and services of soil,

– the range of variations in diversity could be described for agiven pedoclimatic zone and within this zone, for a givenland use. Such information could be used to interpret soilquality analyses for soil users (farmer, industrial or urban),biodiversity erosion, and to improve land use managementwith a view to sustainable development.

Microbial biogeography is therefore relevant at a landscapelevel to understanding soil biodiversity erosion brought aboutby natural and/or anthropogenic activities better. Even if therelationship between soil biodiversity and soil or ecosystemfunctions remains incomplete, such a research strategy shouldimprove soil management in the current context of increasingecosystem goods and services. Consequently, at the Europeanlevel, a better coordination of the different national soil sur-veys and of the strategy employed to characterise biodiversityconstitutes a challenge for the future soil protection policy interms of sustainable development.

Acknowledgements: The ECOMIC-RMQS programme was supportedby the French National Research Agency (ANR) and ADEME. Samplingwas supported by a French Scientific Group of Interest on soils: the “GISSol”, involving the French Ministry for Ecology and Sustainable Development(MEDD), the French Ministry of Agriculture (MAP), the French Institutefor the Environment (IFEN), the French Environment and Energy Manage-ment Agency (ADEME), and the National Institute for Agronomic Research(INRA). We thank all the soil surveyors and technical assistants involved insampling the sites.

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